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Assigned to pje...@biociphers.org by meMar 1, 2021, 12:21:15 PM3/1/21

to majiq_voila

Hi,

Thanks again for such a useful tool.

I have a question regarding the values of psi in an lsv. Thanks to the article you wrote, I understand that the sum of all psi in a LSV must be equal to 1. In general, psi calculation is : #includingreads / (#includingreads + #excludingreads), if I remember well.

So how is it possible that, for example, in a source based LSV such as s|1e1.1o1|1e2.1o1 , that the first junction (which is basically the reference exon being linked to the next exon, without excluding any exon) has a value different from 1 ? Because in this case, the ratio used to calculate psi value, should be for example : 4/4.

Does MAJIQ calculate the psi value of this junction by doing : 1 - (sum(all other junctions in the LSV)) ?

The answer is maybe is the article but I am struggling a bit with the mathmatical formulas. :/

Any help would be highly appreciated !

Have a nice day,

Cheers,

Elsa

Mar 4, 2021, 12:16:47 PM3/4/21

to majiq_voila

Hi Elsa,

If I'm understanding your question correctly, the calculation is not quite as simple as you describe. However, there should not be large discrepancies in a single lsv, where the total is not ~equal to 1.

Can you please post a screenshot of the lsv and values you see for it's junctions, so that I of one of the lab members may be able to easily spot what is happening?

Thanks,

-Paul

Mar 5, 2021, 8:46:21 AM3/5/21

to majiq_voila

Yes apparently the calculation is not that simple... I supposed that the part of the paper that I am interesting in is :

I struggle a little to apply the formula to a practical case. Could you help me for example to understand what would be the calculation of psi for example in this LSV, for the red junction ?

Thank you for the help !

Have a nice day :)

Elsa

Mar 5, 2021, 11:35:32 AM3/5/21

to majiq_voila

Hi Elsa,

I'm going to reach out to some of my colleagues for help with decoding the theoretical question you have, please stand by for that reply.

I also wanted to ask, though, if there was indeed a discrepancy here, with regard to the three psi values not adding to ~1? Could you post the three psi values for grp1 and/or grp2? They are not coming out to be approximately 1, it may be something else I need to investigate.

Thanks,

-Paul

Mar 5, 2021, 1:47:53 PM3/5/21

to majiq_voila

Oh sorry that's my fault, I gave a deltapsi example, was not paying attention.

Here is an example with a psi voila view.

I am interesting on the calculation used to find psi value of the red junction.

Do you need more information about the LSV of interest ?

Elsa

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